Contents
RunLdPred2Rule
LDpred2 model rule
RunLdPred2Rule resolves LDpred2 polygenius.model outputs.
Details
Reactive rule for model outputs generated by algorithm LDpred2.
The rule requests GWAS input at required pval.max, binds an ld.bigsnpr
storage resource for the matched panel/build, matches GWAS variants to that
storage in-process, and then runs LDpred2 in auto, grid, or inf mode.
inf and auto produce one final model. grid produces one dynamic model
output per grid row because PolyGenius does not receive validation data and
should not choose one grid column internally.
User-facing LD construction controls map onto ld.bigsnpr storage fields:
ld.size->windowld.thr->threshold
These controls affect how the upstream bigsnpr LD storage is built. They are
separate from native LDpred2 fitting arguments. Native fitting arguments are
forwarded by name to the selected bigsnpr mode when supported by the
installed bigsnpr version. Missing arguments use the private mode defaults;
required values such as h2 or h2_init are estimated when not supplied.
Super class
PolyGenius::Rule -> RunLdPred2Rule
Methods
Public methods
RunLdPred2Rule$new()RunLdPred2Rule$matches()RunLdPred2Rule$inputs()RunLdPred2Rule$bind()RunLdPred2Rule$requirements()RunLdPred2Rule$run()RunLdPred2Rule$clone()
Method new()
Create the LDpred2 rule.
Usage
RunLdPred2Rule$new()
Method matches()
Check whether this rule can produce the requested output.
Usage
RunLdPred2Rule$matches(output.spec)
Arguments
output.spec — Output resource specification.
Returns
TRUE for LDpred2 model outputs.
Method inputs()
Build input specifications for this output.
Usage
RunLdPred2Rule$inputs(output.spec)
Arguments
output.spec — Output resource specification.
Returns
Named list with gwas and deferred ld input.
Method bind()
Bind LD storage input after GWAS build is known.
Usage
RunLdPred2Rule$bind(inputs, store, output.spec = NULL)
Arguments
inputs — Named list of input specifications.
store — Resource store.
output.spec — Output resource specification.
Returns
Updated named list of inputs.
Method requirements()
Declare resource requirements for this rule.
Usage
RunLdPred2Rule$requirements(output.spec, inputs)
Arguments
output.spec — Output resource specification.
inputs — Bound input values/specifications.
Returns
Named list with cores and memory.
Method run()
Execute LDpred2 model construction.
Usage
RunLdPred2Rule$run(output.spec, inputs, logger = pg.logger())
Arguments
output.spec — Output resource specification.
inputs — Named list of bound input values.
logger — Rule logger.
Returns
Rule result list with data, meta, and logs.
Method clone()
The objects of this class are cloneable with this method.
Usage
RunLdPred2Rule$clone(deep = FALSE)
Arguments
deep — Whether to make a deep clone.
See Also
Other algorithm-rules:
BuildLDBigsnprRule,
BuildLDBlocksRule,
ClumpVariantsRule,
RunLassosum2Rule,
RunPrscsRule,
ThresholdClumpedRule